Stretching an anisotropic DNA

Eslami-Mossallam, Behrouz; Ejtehadi, Mohammad Reza

doi:10.1063/1.2842065

Cited by 14 publications

(20 citation statements)

References 17 publications

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“…In [84], Eslami-Moossallam and Ejtehadi have introduced the following effective Hamiltonian for the description of the dynamics of an anisotropic DNA molecule. (397) is non-Hermitian, but it is at the same time real, i.e., it commutes with the time-reversal operator T .…”

Section: Biophysicsmentioning

confidence: 99%

Pseudo-Hermitian Representation of Quantum Mechanics

Mostafazadeh

2010

Int. J. Geom. Methods Mod. Phys.

865

1,210

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A diagonalizable non-Hermitian Hamiltonian having a real spectrum may be used to define a unitary quantum system, if one modifies the inner product of the Hilbert space properly. We give a comprehensive and essentially self-contained review of the basic ideas and techniques responsible for the recent developments in this subject. We provide a critical assessment of the role of the geometry of the Hilbert space in conventional quantum mechanics to reveal the basic physical principle motivating our study. We then offer a survey of the necessary mathematical tools, present their utility in establishing a lucid and precise formulation of a unitary quantum theory based on a non-Hermitian Hamiltonian, and elaborate on a number of relevant issues of fundamental importance. In particular, we discuss the role of the antilinear symmetries such as PT , the true meaning and significance of the so-called charge operators C and the CPT -inner products, the nature of the physical observables, the equivalent description of such models using ordinary Hermitian quantum mechanics, the pertaining duality between localnon-Hermitian versus nonlocal-Hermitian descriptions of their dynamics, the corresponding classical systems, the pseudo-Hermitian canonical quantization scheme, various methods of calculating the (pseudo-) metric operators, subtleties of dealing with time-dependent quasi-Hermitian Hamiltonians and the path-integral formulation of the theory, and the structure of the state space and its ramifications for the quantum Brachistochrone problem. We also explore some concrete physical applications and manifestations of the abstract concepts and tools that have been developed in the course of this investigation. These include applications in nuclear physics, condensed matter physics, relativistic quantum mechanics and quantum field theory, quantum cosmology, electromagnetic wave propagation, open quantum systems, magnetohydrodynamics, quantum chaos, and biophysics.

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Section: Biophysicsmentioning

confidence: 99%

Pseudo-Hermitian Representation of Quantum Mechanics

Mostafazadeh

2010

Int. J. Geom. Methods Mod. Phys.

865

1,210

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“…κ 1 , κ 2 , and ω) respectively correspond to rotation of the filament aroundd 1 , d 2 , andd 3 and called tilt, roll and twist [21]. Therefore, the elastic energy of an inextensible, unshearable and anisotropic filament in harmonic approximation can be written as [54,60] …”

Section: Fig 2: Parametrization Of the Elastic Rodmentioning

confidence: 99%

“…The sequencedependent bending anisotropy of B-DNA has been observed in X-ray crystallography of DNA-protein complexes [40,41] and NMR spectroscopy [42], as well as allatomistic simulations [43][44][45][46][47][48][49][50]. Many theoretical studies have considered such anisotropic bending into the elastic models [51][52][53][54][55][56], and it is shown that although the bending anisotropy affect the elastic properties of a short DNA molecule in 3D, it becomes unimportant when the DNA segment is long enough to include a few full helical turns [54,57].…”

Section: Figmentioning

confidence: 99%

“…It is well known that, the tangent-tangent correlation function of a free, long and highly twisted anisotropic model in 3D decays as cos θ(L) 3D = exp(−L/P 3D ), where P 3D is given by the harmonic mean of the hard and soft bending rigidities, i.e. A 1 and A 2 , [44,54,69] . Fig 4(B) shows the correlation function in 2D, cos θ(L) 2D = exp(−L/2P 2D ), here a clear dependence on C is evident.…”

Section: A the Elastic Properties Of The Long Anisotropic Chainmentioning

confidence: 99%

“…For a planar DNA (confined in the x-y plane wherê z.d 3 = 0), it is convenient to express the local triads in terms of Euler angles Θ(s) = [α(s), β(s), ψ(s)] (0 < α < 2π, β(s) = π/2, 0 < ψ < 2π) as the following [54]:…”

Section: Fig 2: Parametrization Of the Elastic Rodmentioning

confidence: 99%

See 2 more Smart Citations

Stiffer double-stranded DNA in two-dimensional confinement due to bending anisotropy

Salari¹,

Eslami-Mossallam²,

Ranjbar³

et al. 2016

Phys. Rev. E

Self Cite

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Using analytical approach and Monte-Carlo (MC) simulations, we study the elastic behaviour of the intrinsically twisted elastic ribbons with bending anisotropy, such as double-stranded DNA (dsDNA), in two-dimensional (2D) confinement. We show that, due to the bending anisotropy, the persistence length of dsDNA in 2D conformations is always greater than 3D conformations. This result is in consistence with the measured values for DNA persistence length in 2D and 3D in equal biological conditions. We also show that in 2D, an anisotropic, intrinsically twisted polymer exhibits an implicit twist-bend coupling, which leads to the kink formations with a half helical turn periodicity along the bent polymer.

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Elastic Energy Partitioning in DNA Deformation and Binding to Proteins

Teng

Hwang

2015

ACS Nano

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We study the elasticity of DNA based on local principal axes of bending identified from over 0.9-μs all-atom molecular dynamics simulations of DNA oligos. The calculated order parameters describe motion of DNA as an elastic rod. In 10 possible dinucleotide steps, bending about the two principal axes is anisotropic yet linearly elastic. Twist about the centroid axis is largely decoupled from bending, but DNA tends to overtwist for unbending beyond the typical range of thermal motion, which is consistent with experimentally observed twist-stretch coupling. The calculated elastic stiffness of dinucleotide steps yield sequence-dependent persistence lengths consistent with previous single-molecule experiments, which is further analyzed by performing coarse-grained simulations of DNA. Flexibility maps of oligos constructed from simulation also match with those from the precalculated stiffness of dinucleotide steps. These support the premise that base pair interaction at the dinucleotide-level is mainly responsible for the elasticity of DNA. Furthermore, we analyze 1381 crystal structures of protein-DNA complexes. In most structures, DNAs are mildly deformed and twist takes the highest portion of the total elastic energy. By contrast, in structures with the elastic energy per dinucleotide step greater than about 4.16 kBT (kBT: thermal energy), the major bending becomes dominant. The extensional energy of dinucleotide steps takes at most 35% of the total elastic energy except for structures containing highly deformed DNAs where linear elasticity breaks down. Such partitioning between different deformational modes provides quantitative insights into the conformational dynamics of DNA as well as its interaction with other molecules and surfaces.

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Stretching an anisotropic DNA

Cited by 14 publications

References 17 publications

Pseudo-Hermitian Representation of Quantum Mechanics

Pseudo-Hermitian Representation of Quantum Mechanics

Stiffer double-stranded DNA in two-dimensional confinement due to bending anisotropy

Elastic Energy Partitioning in DNA Deformation and Binding to Proteins

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